Is there a way to put faces on different layers with edit mode?
In edit mode - select the faces you are wanting in a different layer. Shift-D to duplicate them. Then type the shortcut letter P. A menu will appear. Confirm 'Selection'. This will separate the selected faces as a new distinct object when you return to object mode. You can then place the new object (duplicated faces) into any layer you like. 

The 2.8 beta has a new layer mechanism that may support a better version of this application.